processArrayDataObject      package:arrayMagic      R Documentation

_A_u_t_o_m_a_t_e_d _p_r_o_c_e_s_s_i_n_g _a_n_d _n_o_r_m_a_l_i_s_a_t_i_o_n _o_f _a_n _a_r_r_a_y_D_a_t_a-_o_b_j_e_c_t
(_p_a_r_t _o_f _f_u_n_c_t_i_o_n _p_r_o_c_e_s_s_A_r_r_a_y_D_a_t_a)

_D_e_s_c_r_i_p_t_i_o_n:

     Automated processing and normalisation of an 'arrayData'-object.
     The function is called by 'processArrayData'.

_U_s_a_g_e:

     processArrayDataObject(arrayDataObject, spotIdentifier = "Name", verbose = TRUE, normalisationMethod = "vsn", subtractBackground=FALSE, spotsRemovedBeforeNormalisation = NULL, spotsRemovedAfterNormalisation = NULL, subGroups = NULL, channelsSeparately = FALSE, hybridisationGroups = NULL)

_A_r_g_u_m_e_n_t_s:

arrayDataObject: object of class 'arrayData-class'; required; default
          missing 

spotIdentifier: character string; required; default "Name".
          'spotIdentifier' specifies the column in the image analysis
          result files which contain spot or gene identifiers.

 verbose: logical; required; default: 'TRUE' 

normalisationMethod: character string; required; default: "vsn"; cf.
          argument 'method' of 'normalise' 

subtractBackground: logical; required; default: 'FALSE' cf. 'normalise' 

spotsRemovedBeforeNormalisation: vector of character strings; required;
          default 'NULL'. All spots which match the string(s) will be
          excluded   already before normalisation and will not be
          present in the resulting objects at all. 

spotsRemovedAfterNormalisation: vector of character strings; required;
          default: 'NULL'; cf. argument
          'spotsRemovedBeforeNormalisation' 

subGroups: character string or 'NULL'; required; cf. 'normalise';
          default: 'NULL' 

channelsSeparately: logical; required; cf. 'normalise'; default:
          'FALSE'

hybridisationGroups: list of numeric vectors; cf. 'normalise';
          required; default: 'NULL'

_V_a_l_u_e:

     A list of objects, i.e.  an "exprSetRGObject" and and
     "arrayDataObject" with corresponding class types 'exprSetRG-class'
     and 'arrayData-class'.

_A_u_t_h_o_r(_s):

     Andreas Buness <a.buness@dkfz.de>

_S_e_e _A_l_s_o:

     'processArrayData', 'normalise', 'exprSetRG-class',
     'arrayData-class'

_E_x_a_m_p_l_e_s:

            LOADPATH <- file.path(.path.package("arrayMagic"), "extdata")
             SLIDEDESCRIPTIONFILE <- "slideDescription"

            slideDescription <- readpDataSlides(
                                  loadPath=LOADPATH, 
                                  slideDescriptionFile=SLIDEDESCRIPTIONFILE
                                )
             arrayDataObject <- readIntensities(
                                  loadPath=LOADPATH,
                                  slideDescription=slideDescription
                               )

            resultList <- processArrayDataObject( arrayDataObject=arrayDataObject )
              
      

